Job ID = 10845164 sra ファイルのダウンロード中... Completed: 169469K bytes transferred in 17 seconds (81229K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Read 3469095 spots for /home/okishinya/chipatlas/results/dm3/SRX2642380/SRR5345720.sra Written 3469095 spots for /home/okishinya/chipatlas/results/dm3/SRX2642380/SRR5345720.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:21 3469095 reads; of these: 3469095 (100.00%) were unpaired; of these: 491923 (14.18%) aligned 0 times 2051357 (59.13%) aligned exactly 1 time 925815 (26.69%) aligned >1 times 85.82% overall alignment rate Time searching: 00:02:21 Overall time: 00:02:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 191052 / 2977172 = 0.0642 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Wed, 04 Jul 2018 09:29:42: # Command line: callpeak -t SRX2642380.bam -f BAM -g dm -n SRX2642380.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2642380.20 # format = BAM # ChIP-seq file = ['SRX2642380.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 04 Jul 2018 09:29:42: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:29:42: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:29:42: # Command line: callpeak -t SRX2642380.bam -f BAM -g dm -n SRX2642380.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2642380.05 # format = BAM # ChIP-seq file = ['SRX2642380.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 04 Jul 2018 09:29:42: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:29:42: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:29:42: # Command line: callpeak -t SRX2642380.bam -f BAM -g dm -n SRX2642380.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2642380.10 # format = BAM # ChIP-seq file = ['SRX2642380.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Wed, 04 Jul 2018 09:29:42: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:29:42: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:29:50: 1000000 INFO @ Wed, 04 Jul 2018 09:29:50: 1000000 INFO @ Wed, 04 Jul 2018 09:29:50: 1000000 INFO @ Wed, 04 Jul 2018 09:29:58: 2000000 INFO @ Wed, 04 Jul 2018 09:29:59: 2000000 INFO @ Wed, 04 Jul 2018 09:29:59: 2000000 INFO @ Wed, 04 Jul 2018 09:30:05: #1 tag size is determined as 99 bps INFO @ Wed, 04 Jul 2018 09:30:05: #1 tag size = 99 INFO @ Wed, 04 Jul 2018 09:30:05: #1 total tags in treatment: 2786120 INFO @ Wed, 04 Jul 2018 09:30:05: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:30:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:30:05: #1 tags after filtering in treatment: 2786120 INFO @ Wed, 04 Jul 2018 09:30:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:30:05: #1 finished! INFO @ Wed, 04 Jul 2018 09:30:05: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:30:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:30:05: #2 number of paired peaks: 329 WARNING @ Wed, 04 Jul 2018 09:30:05: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Wed, 04 Jul 2018 09:30:05: start model_add_line... INFO @ Wed, 04 Jul 2018 09:30:05: start X-correlation... INFO @ Wed, 04 Jul 2018 09:30:05: end of X-cor INFO @ Wed, 04 Jul 2018 09:30:05: #2 finished! INFO @ Wed, 04 Jul 2018 09:30:05: #2 predicted fragment length is 95 bps INFO @ Wed, 04 Jul 2018 09:30:05: #2 alternative fragment length(s) may be 95 bps INFO @ Wed, 04 Jul 2018 09:30:05: #2.2 Generate R script for model : SRX2642380.10_model.r WARNING @ Wed, 04 Jul 2018 09:30:05: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:30:05: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Wed, 04 Jul 2018 09:30:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:30:05: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:30:05: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:30:05: #1 tag size is determined as 99 bps INFO @ Wed, 04 Jul 2018 09:30:05: #1 tag size = 99 INFO @ Wed, 04 Jul 2018 09:30:05: #1 total tags in treatment: 2786120 INFO @ Wed, 04 Jul 2018 09:30:05: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:30:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:30:05: #1 tags after filtering in treatment: 2786120 INFO @ Wed, 04 Jul 2018 09:30:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:30:05: #1 finished! INFO @ Wed, 04 Jul 2018 09:30:05: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:30:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:30:05: #1 tag size is determined as 99 bps INFO @ Wed, 04 Jul 2018 09:30:05: #1 tag size = 99 INFO @ Wed, 04 Jul 2018 09:30:05: #1 total tags in treatment: 2786120 INFO @ Wed, 04 Jul 2018 09:30:05: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:30:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:30:05: #1 tags after filtering in treatment: 2786120 INFO @ Wed, 04 Jul 2018 09:30:05: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:30:05: #1 finished! INFO @ Wed, 04 Jul 2018 09:30:05: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:30:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:30:05: #2 number of paired peaks: 329 WARNING @ Wed, 04 Jul 2018 09:30:05: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Wed, 04 Jul 2018 09:30:05: start model_add_line... INFO @ Wed, 04 Jul 2018 09:30:05: start X-correlation... INFO @ Wed, 04 Jul 2018 09:30:05: end of X-cor INFO @ Wed, 04 Jul 2018 09:30:05: #2 finished! INFO @ Wed, 04 Jul 2018 09:30:05: #2 predicted fragment length is 95 bps INFO @ Wed, 04 Jul 2018 09:30:05: #2 alternative fragment length(s) may be 95 bps INFO @ Wed, 04 Jul 2018 09:30:05: #2.2 Generate R script for model : SRX2642380.20_model.r WARNING @ Wed, 04 Jul 2018 09:30:06: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:30:06: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Wed, 04 Jul 2018 09:30:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:30:06: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:30:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:30:06: #2 number of paired peaks: 329 WARNING @ Wed, 04 Jul 2018 09:30:06: Fewer paired peaks (329) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 329 pairs to build model! INFO @ Wed, 04 Jul 2018 09:30:06: start model_add_line... INFO @ Wed, 04 Jul 2018 09:30:06: start X-correlation... INFO @ Wed, 04 Jul 2018 09:30:06: end of X-cor INFO @ Wed, 04 Jul 2018 09:30:06: #2 finished! INFO @ Wed, 04 Jul 2018 09:30:06: #2 predicted fragment length is 95 bps INFO @ Wed, 04 Jul 2018 09:30:06: #2 alternative fragment length(s) may be 95 bps INFO @ Wed, 04 Jul 2018 09:30:06: #2.2 Generate R script for model : SRX2642380.05_model.r WARNING @ Wed, 04 Jul 2018 09:30:06: #2 Since the d (95) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:30:06: #2 You may need to consider one of the other alternative d(s): 95 WARNING @ Wed, 04 Jul 2018 09:30:06: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:30:06: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:30:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:30:12: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:30:12: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:30:13: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:30:16: #4 Write output xls file... SRX2642380.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:30:16: #4 Write peak in narrowPeak format file... SRX2642380.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:30:16: #4 Write summits bed file... SRX2642380.20_summits.bed INFO @ Wed, 04 Jul 2018 09:30:16: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (309 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:30:16: #4 Write output xls file... SRX2642380.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:30:16: #4 Write peak in narrowPeak format file... SRX2642380.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:30:16: #4 Write summits bed file... SRX2642380.10_summits.bed INFO @ Wed, 04 Jul 2018 09:30:16: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (544 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:30:16: #4 Write output xls file... SRX2642380.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:30:16: #4 Write peak in narrowPeak format file... SRX2642380.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:30:16: #4 Write summits bed file... SRX2642380.05_summits.bed INFO @ Wed, 04 Jul 2018 09:30:16: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (798 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。